Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Draft Genome Sequence of Escherichia albertii Strain Mex-12/320a, Isolated from an Infant with Diarrhea and Harboring Virulence Genes Associated with Diarrheagenic Strains of Enteropathogenic Escherichia coli

Samantha Maldonado-Puga, Mario Meza-Segura, Adriana Becerra, Mussaret B. Zaidi, Teresa Estrada-Garcia
David Rasko, Editor
Samantha Maldonado-Puga
aDepartment of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mario Meza-Segura
aDepartment of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adriana Becerra
aDepartment of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mussaret B. Zaidi
bInfectious Diseases Research Unit, Hospital General O’Horan, Merida, Mexico
cDepartment of Epidemiology and Biostatistics, Michigan State University, Lansing, Michigan, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Teresa Estrada-Garcia
aDepartment of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Rasko
University of Maryland School of Medicine
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00208-19
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Escherichia albertii is an emerging human enteropathogen. We report the draft genome sequence of E. albertii strain Mex-12/320a, isolated from an infant with diarrhea. The presence of the pathogenic island O122/IE6 and the nleA gene, previously found in diarrheagenic enteropathogenic Escherichia coli strains, suggests that E. albertii may cause acute diarrhea.

ANNOUNCEMENT

Escherichia albertii is an emerging human enteropathogen which belongs to the attaching and effacing (A/E) family of gastrointestinal pathogens that include well-known human pathogens such as enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (1). The genes responsible for the A/E phenotype are carried on a pathogenicity island (PAI) known as the locus of enterocyte effacement (LEE), which encodes several effector proteins that are all injected into the host cell by the type III secretion system (T3SS) (2). Other non-LEE-encoded (NLE) EPEC effectors are translocated by the T3SS (1). EPEC non-LEE genes, such as nleA and those harbored in the PAI O122/IE6 (efa1 or lifA, espL, nleB, and nleE), are significantly more prevalent among EPEC strains isolated from children with diarrhea than in those without (3–5). Most of these genes are involved in bacterial evasion of the host innate immune response (6, 7).

We report the draft genome sequence of E. albertii strain Mex-12/320a, a lactose-negative E. coli strain that was isolated from the stool of a 2-year-old girl with acute diarrhea. She was admitted to a hospital in Yucatan, Mexico, in 2012 for dehydration after 4 days of illness with 4 stool movements per day and 12 episodes of vomiting. This strain was isolated and characterized as previously described (8), was originally classified as atypical EPEC, and was the sole pathogenic isolate identified in the fecal sample. It was subsequently reclassified as E. albertii by a multiplex in silico PCR that discriminates between different Escherichia species using primers for the DNA-binding transcriptional activator of a cysteine biosynthesis gene (393-bp product) that appears to be specific to this species (9).

One colony from MacConkey agar was selected and incubated in LB broth for 18 h at 37°C without agitation. Genomic DNA was extracted using a phenol-chloroform protocol, prepared as Illumina sequencing libraries using the Nextera XT kit, and sequenced by the GAIIx system (Illumina, San Diego, CA, USA), generating 3,148,027 reads. Quality control, trimming, and filtering of raw sequencing data were performed with Trim Galore v0.4.1 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The genome was assembled de novo using the SPAdes genome assembler v3.9.1 (http://cab.spbu.ru/software/spades/), and the accuracy of the genome assemblies was evaluated with REAPR 1.0.16 (10). Protein-coding sequences and RNA genes were predicted, and functional annotation was performed with Prokka v1.11. Preassembled contigs were scaffolded using SSPACE_Standard_v3.0.pl (11), and gaps were closed with GapFiller_v1-10 (12). Default parameters were used for all software during the assembly and annotation process.

The draft chromosome sequence of E. albertii strain Mex-12/320a consists of 4,941,694 bp in 268 scaffolds, with an N50 value 130,167 bp, a maximum scaffold size of 341 kbp, and 49.54% G+C content. The genome contains 5,090 predicted genes, of which 4,763 are coding sequences (CDSs), 5 are rRNA (rrn) operons, and 79 are tRNA genes. The genome sequence confirmed the presence of not only the LEE genes but also nleA and cdt-II (cytolethal distending toxin II) virulence genes previously found in other E. albertii strains (13, 14). To the best of our knowledge, this is the first report of the presence of the complete PAI O122/IE6 (efa1 or lifA, espL, nleB, and nleE genes) in an E. albertii strain.

This work confirms that the E. albertii Mex-12/320a genome harbors virulence genes that have been previously reported in EPEC isolates from children with diarrhea. This finding adds to the growing body of evidence that E. albertii is an emerging pathogen of diarrheal disease (15) and that nleA and the PAI O122/IE6 are virulence markers of A/E Escherichia pathogens. This report, in conjunction with those for other genomes of E. albertii (13, 16, 17), will contribute to a greater understanding of the phylogeny and evolution of Escherichia species and to the identification of new virulence factors among A/E bacteria.

Data availability.The draft genome assembly of E. albertii strain Mex-12/320a was deposited in DDBJ/ENA/GenBank under the accession number SIZV00000000 and BioProject number PRJNA523447. Sequencing reads for E. albertii strain Mex-12/320a have been deposited in the NCBI Sequence Read Archive (SRA) under the accession number SRR9024355.

ACKNOWLEDGMENTS

This work was supported by CONACYT scholarships to S.M.-P. (award 261205), M.M.-S. (award 368026), and A.B. (award 483617) and a CONACYT grant (254994) to T.E.-G.

FOOTNOTES

    • Received 5 March 2019.
    • Accepted 4 June 2019.
    • Published 3 July 2019.
  • Copyright © 2019 Maldonado-Puga et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Slater SL,
    2. Sågfors AM,
    3. Pollard DJ,
    4. Ruano-Gallego D,
    5. Frankel G
    . 2018. The type III secretion system of pathogenic Escherichia coli. Curr Top Microbiol Immunol 416:51–72. doi:10.1007/82_2018_116.
    OpenUrlCrossRef
  2. 2.↵
    1. Gaytán MO,
    2. Martínez-Santos VI,
    3. Soto E,
    4. González-Pedrajo B
    . 2016. Type three secretion system in attaching and effacing pathogens. Front Cell Infect Microbiol 6:129. doi:10.3389/fcimb.2016.00129.
    OpenUrlCrossRef
  3. 3.↵
    1. Afset JE,
    2. Bruant G,
    3. Brousseau R,
    4. Harel JJ,
    5. Anderssen E,
    6. Bevanger L,
    7. Bergh KK
    . 2006. Identification of virulence genes linked with diarrhea due to atypical enteropathogenic Escherichia coli by DNA microarray analysis and PCR. J Clin Microbiol 44:3703–3711. doi:10.1128/JCM.00429-06.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Mercado EH,
    2. Piscoche C,
    3. Contreras C,
    4. Durand D,
    5. Riveros M,
    6. Ruiz J,
    7. Ochoa TJ
    . 2016. Pathogenicity island O-122 in enteropathogenic Escherichia coli strains is associated with diarrhea severity in children from Lima Peru. Int J Med Microbiol 306:231–236. doi:10.1016/j.ijmm.2016.05.005.
    OpenUrlCrossRef
  5. 5.↵
    1. Salvador FA,
    2. Hernandes RT,
    3. Vieira MAM,
    4. Rockstroh AC,
    5. Gomes T
    . 2014. Distribution of non-LEE-encoded type 3 secretion system dependent effectors in enteropathogenic Escherichia coli. Braz J Microbiol 45:851–855. doi:10.1590/S1517-83822014000300014.
    OpenUrlCrossRef
  6. 6.↵
    1. Santos AS,
    2. Finlay BB
    . 2015. Bringing down the host: enteropathogenic and enterohaemorrhagic Escherichia coli effector‐mediated subversion of host innate immune pathways. Cell Microbiol 17:318–332. doi:10.1111/cmi.12412.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Yen H,
    2. Sugimoto N,
    3. Tobe T
    . 2015. Enteropathogenic Escherichia coli uses NleA to inhibit NLRP3 inflammasome activation. PLoS Pathog 11:e1005121. doi:10.1371/journal.ppat.1005121.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Patzi-Vargas S,
    2. Zaidi MB,
    3. Perez-Martinez I,
    4. León-Cen M,
    5. Michel-Ayala A,
    6. Chaussabel D,
    7. Estrada-Garcia T
    . 2015. Diarrheagenic Escherichia coli carrying supplementary virulence genes are an important cause of moderate to severe diarrhoeal disease in Mexico. PLoS Negl Trop Dis 9:e0003510. doi:10.1371/journal.pntd.0003510.
    OpenUrlCrossRefPubMed
  9. 9.↵
    1. Lindsey RL,
    2. Garcia-Toledo L,
    3. Fasulo D,
    4. Gladney LM,
    5. Strockbine N
    . 2017. Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii. J Microbiol Methods 140:1–4. doi:10.1016/j.mimet.2017.06.005.
    OpenUrlCrossRef
  10. 10.↵
    1. Hunt M,
    2. Kikuchi T,
    3. Sanders M,
    4. Newbold C,
    5. Berriman M,
    6. Otto TD
    . 2013. REAPR: a universal tool for genome assembly evaluation. Genome Biol 14:R47. doi:10.1186/gb-2013-14-5-r47.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Boetzer M,
    2. Pirovano W
    . 2012. Toward almost closed genomes with GapFiller. Genome Biol 13:R56. doi:10.1186/gb-2012-13-6-r56.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Boetzer M,
    2. Henkel CV,
    3. Jansen HJ,
    4. Butler D,
    5. Pirovano W
    . 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579. doi:10.1093/bioinformatics/btq683.
    OpenUrlCrossRefPubMedWeb of Science
  13. 13.↵
    1. Ooka T,
    2. Ogura Y,
    3. Katsura K,
    4. Seto K,
    5. Kobayashi H,
    6. Kawano K,
    7. Tokuoka E,
    8. Furukawa M,
    9. Harada S,
    10. Yoshino S,
    11. Seto J,
    12. Ikeda T,
    13. Yamaguchi K,
    14. Murase K,
    15. Gotoh Y,
    16. Imuta M,
    17. Nishi J,
    18. Gomes TA,
    19. Beutin L,
    20. Hayashi T
    . 2015. Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli. Genome Biol Evol 7:3170–3179. doi:10.1093/gbe/evv211.
    OpenUrlCrossRefPubMed
  14. 14.↵
    1. Hinenoya A,
    2. Yasuda N,
    3. Hibino T,
    4. Shima A,
    5. Nagita A,
    6. Tsukamoto T,
    7. Yamasaki S
    . 2017. Isolation and characterization of an Escherichia albertii strain producing three different toxins from a child with diarrhea. Jpn J Infect Dis 70:252–257. doi:10.7883/yoken.JJID.2016.186.
    OpenUrlCrossRef
  15. 15.↵
    1. Huys G,
    2. Cnockaert M,
    3. Janda JM,
    4. Swings J
    . 2003. Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children. Int J Syst Evol Microbiol 53:807–810. doi:10.1099/ijs.0.02475-0.
    OpenUrlCrossRefPubMedWeb of Science
  16. 16.↵
    1. Murakami K,
    2. Etoh Y,
    3. Tanaka E,
    4. Ichihara S,
    5. Horikawa K,
    6. Kawano K,
    7. Ooka T,
    8. Kawamura Y,
    9. Ito K
    . 2014. Shiga toxin 2f-producing Escherichia albertii from a symptomatic human. Jpn J Infect Dis 67:204–208. doi:10.7883/yoken.67.204.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Romão FT,
    2. Hernandes RT,
    3. Ooka T,
    4. Hayashi T,
    5. Sperandio V,
    6. Gomes TAT
    . 2018. Complete genome sequence of Escherichia albertii strain 1551-2, a potential extracellular and intracellular pathogen. Genome Announc 6:e00075-18. doi:10.1128/genomeA.00075-18.
    OpenUrlCrossRef
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Escherichia albertii Strain Mex-12/320a, Isolated from an Infant with Diarrhea and Harboring Virulence Genes Associated with Diarrheagenic Strains of Enteropathogenic Escherichia coli
Samantha Maldonado-Puga, Mario Meza-Segura, Adriana Becerra, Mussaret B. Zaidi, Teresa Estrada-Garcia
Microbiology Resource Announcements Jul 2019, 8 (27) e00208-19; DOI: 10.1128/MRA.00208-19

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Draft Genome Sequence of Escherichia albertii Strain Mex-12/320a, Isolated from an Infant with Diarrhea and Harboring Virulence Genes Associated with Diarrheagenic Strains of Enteropathogenic Escherichia coli
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Draft Genome Sequence of Escherichia albertii Strain Mex-12/320a, Isolated from an Infant with Diarrhea and Harboring Virulence Genes Associated with Diarrheagenic Strains of Enteropathogenic Escherichia coli
Samantha Maldonado-Puga, Mario Meza-Segura, Adriana Becerra, Mussaret B. Zaidi, Teresa Estrada-Garcia
Microbiology Resource Announcements Jul 2019, 8 (27) e00208-19; DOI: 10.1128/MRA.00208-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X